Programmatic Access to Web-Based Chemical Information – Examples

Sources

File types available from sources are given in parentheses.

[CDK] https://ws1.bmc.uu.se/cdk (XML)
[CDKD] CDK-Depict (SVG)
[CIR] NCI/CADD Chemical Identifier Resolver (TXT, SDF, GIF)
[CIP] TOXNET ChemicalIDplus (HTML only; no API)*
[CS] ChemSpider (XML, PNG)*
[NWB] NIST Web Book (HTML only; no API)*
[PCE] PubChem E-Util (JSON, XML)
[PCR] PubChem PUG REST (TXT, CSV, XML, JSON, JSONP, SDF, PNG)
[WK] Wikipedia (JSON, JSONP, XML)

* no direct JavaScript access (site does not allow direct access via AJAX; JavaScript and JSmol both use a proxy server)

Examples

1. Tasks that are solved with a single API call which returns the response in plain text or as a single object without any need of parsing or further processing

    1.1 Obtaining an InChI from a name or other chemical identifier
        1.1.1 [CIR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/CADD_InChI_JS.htm
        1.1.2 [CIR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/CADD_InChI_Jmol.htm
        1.1.3 [PCR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_InChI_JS.htm
        1.1.4 [PCR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/PubChem_InChI_Jmol.htm
        1.1.5 [CIR] MS Excel (from 2013): https://drive.google.com/file/d/0B5ln9gFZnHD4YUVmOTZmWWJiS2c
        1.1.6 [CIR] LO Calc: https://drive.google.com/file/d/0B5ln9gFZnHD4ZFgyanNrVlN3ME0
        1.1.7 [CIR] Google Sheets: https://docs.google.com/spreadsheets/d/1q4MyOfu8x7ocNke6vq0uOP_P8CNAK-fIIK0cyyggJPo/copy
        1.1.8 [CIR] Google Scripts: https://docs.google.com/spreadsheets/d/10odN2Fr406sZdNpoFEUFexPeTBe7ENoUColxYcHEOj0/copy
        1.1.9 [PCR] Google Scripts: https://docs.google.com/spreadsheets/d/18r_EJxmKsKaPCOoHwzyiWJDoWU31lXOEMtswPc_3Vrk/copy
        1.1.10 [CIR] Python: http://www.codeskulptor.org/#user41_g77tnnbEBT_2.py

    1.2 Obtaining a list of known chemical names from a name or other chemical identifier
        1.2.1 [CIR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/CADD_Names_JS.htm
        1.2.2 [CIR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/CADD_Names_Jmol.htm
        1.2.3 [PCR] JavaScript: https://drive.google.com/file/d/0B5ln9gFZnHD4TVV5NXlxcVI2dU0

    1.3 Obtaining an SDF file from a name or other chemical identifier
        1.3.1 [CIR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/CADD_SDF_JS.htm
        1.3.2 [CIR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/CADD_SDF_Jmol.htm
        1.3.3 [PCR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_SDF_JS.htm
        1.3.4 [PCR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/PubChem_SDF_Jmol.htm

    1.4 Obtaining a chemical structure drawing as an image from a name or other chemical identifier
        1.4.1 [CIR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/CADD_image_JS.htm
        1.4.2 [CIR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/CADD_image_Jmol.htm
        1.4.3 [PCR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_image_JS.htm
        1.4.4 [PCR] JSmol: https://chemapps.stolaf.edu/olcc/examples/jmol/PubChem_image_Jmol.htm

    1.5 Obtaining a chemical structure drawing as a vector image from a SMILES:
        1.5.1 [CDKD] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/CDK_image_JS.htm (SVG from SMILES)

2. Tasks that are solved with a single API call that returns the response as a structured text file (tablular data, CSV, HTML) or data structure (XML, JSON)

    2.1 Find a CAS Registry Number from a name or other chemical identifier
        2.1.1 [NWB] MS Excel: https://drive.google.com/file/d/0B5ln9gFZnHD4MUdkWWd5SlpTRUk
        2.1.2 [NWB] LO Calc: https://drive.google.com/file/d/0B5ln9gFZnHD4eVd0R2xHeFYwWlk
        2.1.3 [NWB] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/NIST_CASRN_JS.htm

    2.2 Find the boiling point from a CAS Registry Number
        2.2.1 [CIP] Google Sheets: https://docs.google.com/spreadsheets/d/1qrxQiiDG_rlUhPccEkzUowKYEml21EMlmXWEGLOqc0Q/copy (as XML)
        2.2.2 [CIP] VBA: https://drive.google.com/file/d/0B5ln9gFZnHD4aFR5aGVOUTB0aHc (as string data)
        2.2.3 [CIP] Javascript: https://chemapps.stolaf.edu/olcc/examples/js/CIP_BP_JS.htm (as XML)

3. Tasks that are solved using more than one API call in sequence

    3.1 Information for compounds with specific properties or ranges of properties
         3.1.1 [PCE] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_EUtil_JS.htm
         3.1.2 [PCE/PCR] Google Script: https://docs.google.com/spreadsheets/d/1KUV3kbNWZ-ED57-E-J-J1MMOim1ljmz_MyaFuae6QUg/copy

    3.2 Obtaining a ChemSpider ID from a name or other chemical identifier
         3.2.1 [CIR/CS] MS Excel (from 2013): https://drive.google.com/file/d/0B5ln9gFZnHD4UUJscFNGQ0pqQU0
         3.2.2 [CIR/CS] JSmol: https://chemapps.stolaf.edu/olcc/examples/js/CS_image2_JS.htm

    3.3 Download an IR spectrum from a compound name (using NIST)
         3.3.1 [NWB] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/NIST_IR_JS.htm

    3.4 Download a IR/Mass/UVVis spectrum from a SMILES (using NIST)
         3.4.1 [PCR/CIP/NWB] Google Sheets: https://docs.google.com/spreadsheets/d/1iKEXWUk4JQQdueklu8-PFbg-b0GNHYC9hIvoywEOY4I/copy
             (note the document includes a minimal script with a user-defined function to do URI-encoding)

    3.5 Do two SMILES correspond to the same molecule?
         3.5.1 [CIR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/SMILES_Match_JS.htm

4. Tasks that involve using a single API that returns multiple responses, which need to be processed using an array, list, or object

   4.1 Information for compounds with specific properties or ranges of properties
         4.1.1 [PCE] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_EUtil_JS.htm

   4.2 Search for the translation of a compound name to a different languages
         4.2.1 [WK] JavaScript: https://drive.google.com/file/d/0B5ln9gFZnHD4UUlOMjZzTHptZ28

5. Tasks that involve an asynchronous queued request that requires polling of the server to determine completion

   5.1 Find the isomers of a compound from a name or molecular formula

         5.1.1 [PCR] VBA: https://drive.google.com/file/d/0B5ln9gFZnHD4VjZTVkw5RlZkc0k
         5.1.2 [PCR] JavaScript: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_Polling_JS.htm

             (but see nonpolling example that accomplishes the same: https://chemapps.stolaf.edu/olcc/examples/js/PubChem_Fast_JS.htm)

Useful Web Tools

Structure drawings from SMILES, with SMARTS-based highlighting https://chemapps.stolaf.edu/olcc/examples/cdk/depict/cdk_depict.htm

Interconverting 2D and 3D using SMILES https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm